biswebnode/bin/bw_segmentimage.xml

A node.js implementation of BioImage Suite Web command line tools in Javascript and WebAssembly

<?xml version="1.0" encoding="utf-8"?>
<executable>
	<category>BisWEB</category>
	<title>Segment Image</title>
	<description>Performs image segmentation using a histogram-based method if smoothness = 0.0 or using plus mrf segmentation if smoothness > 0.0</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>Zach Saltzman and Xenios Papademetris</contributor>

<acknowledgements>Funding for this work was provided by the NIH Brain Initiative under grant R24 MH114805.</acknowledgements>
	<parameters>
		<label>Standard</label>
		<description>Standard Parameters</description>
		<integer>
			<name>Num Classes</name>
			<label>Num Classes</label>
			<description>Number of classes to segment image into</description>
			<longflag>--numclasses</longflag>
			<default>3</default>
			<constraints>
				<minimum>2</minimum>
				<maximum>8</maximum>
			</constraints>
		</integer>
		<integer>
			<name>Number of Bins</name>
			<label>Number of Bins</label>
			<description>Number of bins in the histogram</description>
			<longflag>--numbins</longflag>
			<default>256</default>
			<constraints>
				<minimum>32</minimum>
				<maximum>1024</maximum>
			</constraints>
		</integer>
		<double>
			<name>Smoothness</name>
			<label>Smoothness</label>
			<description>If > 0 then apply spatial regularization MRF model with this value as the weight</description>
			<longflag>--smoothness</longflag>
			<default>0</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>100</maximum>
			</constraints>
		</double>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<double>
			<name>Maximum Sigma Ratio</name>
			<label>Maximum Sigma Ratio</label>
			<description>Enforced ratio between minimum and maximum standard deviation between class parameters</description>
			<longflag>--maxsigmaratio</longflag>
			<default>0.2</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>1</maximum>
			</constraints>
		</double>
		<string-enumeration>
			<name>Robust</name>
			<label>Robust</label>
			<description>Use robust range algorithm to eliminate outliers prior to segmentation</description>
			<longflag>--robust</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>Smooth Histogram</name>
			<label>Smooth Histogram</label>
			<description>Whether or not to apply smoothing to the histogram</description>
			<longflag>--smoothhisto</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<double>
			<name>MRF Convergence</name>
			<label>MRF Convergence</label>
			<description>Convergence parameter for the MRF iterations</description>
			<longflag>--mrfconvergence</longflag>
			<default>0.2</default>
			<constraints>
				<minimum>0.01</minimum>
				<maximum>0.5</maximum>
			</constraints>
		</double>
		<integer>
			<name>MRF Iterations</name>
			<label>MRF Iterations</label>
			<description>Number of MRF iterations</description>
			<longflag>--mrfiterations</longflag>
			<default>8</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>20</maximum>
			</constraints>
		</integer>
		<integer>
			<name>Internal Iterations</name>
			<label>Internal Iterations</label>
			<description>Number of internal iterations</description>
			<longflag>--internaliterations</longflag>
			<default>4</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>20</maximum>
			</constraints>
		</integer>
		<double>
			<name>Noise Sigma</name>
			<label>Noise Sigma</label>
			<description>Estimate of the standard deviation of noise in the image. This is used to add robustness to the algorithm</description>
			<longflag>--noisesigma2</longflag>
			<default>0</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>1000</maximum>
			</constraints>
		</double>
		<string-enumeration>
			<name>Debug</name>
			<label>Debug</label>
			<description>Toggles debug logging</description>
			<longflag>--debug</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>SlicerProgress</name>
			<label>SlicerProgress</label>
			<description>Enables progress xml outputs for Slicer</description>
			<longflag>--slicerprogress</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
	</parameters>
	<parameters>
		<label>Inputs</label>
		<description>Input Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Input Image</name>
			<label>Input Image</label>
			<description>The filename for the image to be processed</description>
			<longflag>--input</longflag>
    			<channel>input</channel>
		</image>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Output Image</name>
			<label>Output Image</label>
			<description>The output image filename</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>